Bottom currents interacting with topography of sandy sediments cause fluid exchange between the upper sediment layers and the overlying water. In flume experiments we demonstrate that these interfacial water currents transport suspended algae into permeable sediment. Oxygen distribution within the sediment was used to trace advective pore water exchange and the effect of organic matter input. We show the topography-related distribution of organic matter within the sediment and quantify the impact of biogenic and current generated topography on organic matter flux. An in-situ experiment in an intertidal sand flat indicates that the process observed in the laboratory flume is also important for organic matter flux in the natural environment. We conclude that hydrodynamically induced transport provides a direct pathway for fresh suspended organic matter into deeper layers of permeable marine sea beds.